SDRF-Proteomics

1. Introduction

This document provides an overview of tools that support the SDRF-Proteomics format. These tools are developed by the community to help researchers create, validate, and use SDRF files in their proteomics workflows.

The tools are organized into three categories:

  • Annotators: Tools for creating and editing SDRF files

  • Validators: Tools for validating SDRF files against the specification

  • Analysis Tools: Proteomics analysis pipelines that accept SDRF as input

2. Annotators

Annotator tools help researchers create SDRF files from scratch or from existing metadata. These tools typically provide user-friendly interfaces to guide users through the annotation process.

2.1. lesSDRF

lesSDRF is a web-based tool for creating SDRF files with minimal effort.

Feature Description

Type

Web application

URL

https://lessdrf.streamlit.app/

Description

A streamlined web interface for creating SDRF-Proteomics files. The tool guides users through the annotation process with an intuitive form-based interface, reducing the complexity of manual SDRF creation.

Key Features

  • Interactive web-based interface

  • Template-based annotation

  • Real-time validation feedback

  • Export to SDRF-Proteomics format

Publication

Claeys T, Van Den Bossche T, Perez-Riverol Y, Gevaert K, Vizcaíno JA, Martens L. lesSDRF is more: maximizing the value of proteomics data through streamlined metadata annotation. Nature Communications 14, 6743 (2023).

2.2. CupCAKE

CupCAKE (Curation Portal for Curation, Annotation, and Knowledge Extraction) is a comprehensive platform for proteomics data annotation.

Feature Description

Type

Web application

Demo URL

https://cupcake-vanilla-demo.proteo.nexus/

Demo Credentials

Username: demo / Password: demo123

Description

CupCAKE provides a web-based platform for annotating proteomics datasets with standardized metadata. It supports SDRF-Proteomics format and helps users create well-annotated sample metadata files.

Key Features

  • Web-based annotation interface

  • Support for multiple proteomics templates (human, vertebrates, plants, cell-lines, etc.)

  • Integration with ontology services (OLS, Cellosaurus)

  • Batch annotation capabilities

  • SDRF file export and validation

  • Project management and collaboration features
Testing CupCAKE

To try CupCAKE with the demo instance:

  1. Navigate to https://cupcake-vanilla-demo.proteo.nexus/

  2. Log in with username demo and password demo123

  3. Create a new project or explore existing annotated datasets

  4. Use the annotation interface to create SDRF files with guided templates

  5. Export your annotations in SDRF-Proteomics format

3. Validators

Validator tools check SDRF files against the SDRF-Proteomics specification to ensure they are correctly formatted and contain all required information.

3.1. sdrf-pipelines

sdrf-pipelines is the official validation tool for SDRF-Proteomics files.

Feature Description

Type

Python command-line tool / library

Repository

https://github.com/bigbio/sdrf-pipelines

Installation

pip install sdrf-pipelines

Description

The official SDRF-Proteomics validator developed by the community. It validates SDRF files against the specification, checks ontology terms, and ensures data consistency.

Key Features

  • Command-line interface for batch validation

  • Python library for programmatic access

  • Template-specific validation rules

  • Ontology term validation via OLS

  • Detailed error reporting

Publication

Dai C., et al. A proteomics sample metadata representation for multiomics integration and big data analysis. Nature Communications 12, 5854 (2021).
Basic Usage
# Install the validator
pip install sdrf-pipelines

# Validate an SDRF file
parse_sdrf validate-sdrf --sdrf_file sample.sdrf.tsv

# Validate with a specific template
parse_sdrf validate-sdrf --sdrf_file sample.sdrf.tsv --template human

4. Analysis Tools

These tools use SDRF files as input for proteomics data analysis, enabling automated and reproducible workflows.

4.1. quantms

quantms is a comprehensive proteomics analysis pipeline that uses SDRF-Proteomics for experiment annotation.

Feature Description

Type

Nextflow pipeline

Website

https://quantms.org/

Repository

https://github.com/bigbio/quantms

Description

quantms is a Nextflow-based pipeline for quantitative mass spectrometry data analysis. It uses SDRF-Proteomics files to automatically configure the analysis workflow, including sample grouping, labeling schemes, and experimental design.

Key Features

  • Automated workflow configuration from SDRF

  • Support for label-free and labeled quantification (TMT, iTRAQ)

  • DDA and DIA analysis support

  • Reproducible analysis with containerized tools

  • Cloud-ready deployment

Publication

Dai C, Pfeuffer J, Wang H, et al. quantms: a cloud-based pipeline for quantitative proteomics enables the reanalysis of public proteomics data. Nature Methods 21, 1603–1607 (2024).
SDRF Integration

The quantms pipeline reads the SDRF file to automatically:

  • Extract sample-to-file mappings

  • Configure labeling channels for multiplexed experiments

  • Set up experimental factors for statistical analysis

  • Apply appropriate search parameters based on metadata

4.2. Wombat-P

Wombat-P (WOrkflow Metrics, Benchmarking and AnalyTics in Proteomics) is a platform for automated benchmarking and comparison of proteomics workflows.

Feature Description

Type

Nextflow-based benchmarking platform

Repository

https://github.com/wombat-p

Description

Wombat-P provides automated benchmarking and comparison of commonly used bottom-up label-free proteomics workflows. It simplifies the processing of public data by utilizing SDRF-Proteomics as input, streamlining the analysis of annotated local or public ProteomeXchange datasets.

Key Features

  • Automated workflow benchmarking

  • SDRF-based experiment configuration

  • Integration with common proteomics tools

  • Modular and extensible architecture

  • Quality metrics computation

Publication

Bouyssié D, Altıner P, Capella-Gutierrez S, et al. WOMBAT-P: Benchmarking Label-Free Proteomics Data Analysis Workflows. Journal of Proteome Research 23(1), 418-429 (2024).

4.3. MaxQuant

MaxQuant is a widely used proteomics software platform with integrated SDRF metadata support.

Feature Description

Type

Desktop application

Website

https://www.maxquant.org/

Description

MaxQuant is a quantitative proteomics software package designed for analyzing large mass spectrometric datasets. It includes integrated SDRF metadata support, providing a user-friendly way to export metadata in SDRF format for standardized data annotation and repository submission.

Key Features

  • SDRF-compliant metadata export

  • User-friendly metadata annotation interface

  • Integrated with MaxQuant analysis workflow

  • Facilitates ProteomeXchange submissions

Publication

Viegener W, Urazbakhtin S, Ferretti D, et al. Facilitating analysis and dissemination of proteomics data through metadata integration in MaxQuant. Nature Communications 16, 8421 (2025).

5. Contributing Tools

If you have developed a tool that supports SDRF-Proteomics and would like to have it listed here, please:

  1. Open an issue on the GitHub repository

  2. Provide a description of your tool, its main features, and how it supports SDRF-Proteomics

  3. Include links to the tool’s website and/or repository

We welcome contributions from the community to expand the SDRF-Proteomics ecosystem.

6. Additional Resources